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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCGCCCATGGCGACGCCGCCGCCGGCGGCGACGGCGTCCGCGCTTCCCAAGTCTGGGGCGGTATCCAAGGGCTACAACTTTGCATCCACTTGGGAACAGgttggtcgccacgctttcgcttctggcagatctggccgtggctgggcccgagatctcgctggtgcgatcgggtgtttcatggatctgacgctctatttgtttgggcattctggcccttttacag

Basic information

species Zea mays
transcript GRMZM5G825854_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G825854_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA17G04990.1 (Glycine max), 5'ss of exon 1
CGCGCCCATGGCGACGCCGCCGCCGGCGGCGACGGCGTCCGCGCTTCCCAAGTCTGGGGCGGTATCCAAGGGCTACAACTTTGCATCCACTTGGGAACAGgttggtcgccacgctttcgcttctggcagatctggccgtggctgggcccgagatctcgctggtgcgatcgggtgtttcatggatctgacg--ctctatttgtttgggcattctggcccttttacag
       |||| || || |  | |  |  | |   | |||         || || |  ||  | |||||||| |||||||| || ||||||||||||||||||             ||  | ||    |||    ||     |    |    || ||  || |   |||   | |||| | | |||      ||| |||||| | |   |  |             
-------ATGG-GAAGCAGAGGTCCACCTCAATCCCATCCA--------AATTCCGCTGCCATTTCCAAGGGTTACAACTTCGCTTCCACTTGGGAACAGgtt-------------tccttcctcaacgattattccccaaatcacgcttccatttctgtgtttttatc--ttctttcctcgctctagttacctcgatttgtatagatctcgtat-----------
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|211087679|gb|FL052576.1|FL052576
EST:     AGTCTGGGGCGGTATCCAAGGGCTACAACTTTGCATCCACTTGGGAACAG                         AGCGCGCCGCTCACGGAGCAGCAGAAGGCCGCGATCGCCGCGCTCTCCCAC
genomic: AGTCTGGGGCGGTATCCAAGGGCTACAACTTTGCATCCACTTGGGAACAGgttggtcgcc ... ccttttacagAGCGCGCCGCTCACGGAGCAGCAGAAGGCCGCGATCGCCGCGCTCTCCCAC
EST: gi|93281267|gb|EB673531.1|EB673531
EST:     AGTCTGGGGCGGTATCCAAGGGCTACAACTTTGCATCCACTTGGGAACAG                         AGCGCGCCGCTCACGGAGCAGCAGAAGGCCGCGATCGCCGCGCTCTCCCAC
genomic: AGTCTGGGGCGGTATCCAAGGGCTACAACTTTGCATCCACTTGGGAACAGgttggtcgcc ... ccttttacagAGCGCGCCGCTCACGGAGCAGCAGAAGGCCGCGATCGCCGCGCTCTCCCAC
EST: gi|211087678|gb|FL052575.1|FL052575
EST:     AGTCTGGGGCGGTATCCAAGGGCTACAACTTTGCATCCACTTGGGAACAG                         AGCGCGCCGCTCACGGAGCAGCAGAAGGCCGCGATCGCCGCGCTCTCCCAC
genomic: AGTCTGGGGCGGTATCCAAGGGCTACAACTTTGCATCCACTTGGGAACAGgttggtcgcc ... ccttttacagAGCGCGCCGCTCACGGAGCAGCAGAAGGCCGCGATCGCCGCGCTCTCCCAC
EST: gi|149104241|gb|EE289677.2|EE289677
EST:     AGTCTGGGGCGGTATCCAAGGGCTACAACTTTGCATCCACTTGGGAACAG                         AGCGCGCCGCTCACGGAGCAGCAGAAGGCCGCGATCGCCGCGCTCTCCCAC
genomic: AGTCTGGGGCGGTATCCAAGGGCTACAACTTTGCATCCACTTGGGAACAGgttggtcgcc ... ccttttacagAGCGCGCCGCTCACGGAGCAGCAGAAGGCCGCGATCGCCGCGCTCTCCCAC
EST: gi|211087686|gb|FL052583.1|FL052583
EST:     AGTCTGGGGCGGTATCCAAGGGCTACAACTTTGCATCCACTTGGGAACAG                         AGCGCGCCGCTCACGGAGCAGCAGAAGGCCGCGATCGCCGCGCTCTCCCAC
genomic: AGTCTGGGGCGGTATCCAAGGGCTACAACTTTGCATCCACTTGGGAACAGgttggtcgcc ... ccttttacagAGCGCGCCGCTCACGGAGCAGCAGAAGGCCGCGATCGCCGCGCTCTCCCAC
EST: gi|148952057|gb|EC897846.2|EC897846
EST:     AGTCTGGGGCGGTATCCAAGGGCTACAACTTTGCATCCACTTGGGAACAG                         AGCGCGCCGCTCACGGAGCAGCAGAAGGCCGCGATCGCCGCGCTCTCCCAC
genomic: AGTCTGGGGCGGTATCCAAGGGCTACAACTTTGCATCCACTTGGGAACAGgttggtcgcc ... ccttttacagAGCGCGCCGCTCACGGAGCAGCAGAAGGCCGCGATCGCCGCGCTCTCCCAC
EST: gi|91872014|gb|EB401971.1|EB401971
EST:     AGTCTGGGGCGGTATCCAAGGGCTACAACTTTGCATCCACTTGGGAACAG                         AGCGCGCCGCTCACGGAGCAGCAGAAGGCCGCGATCGCCGCGCTCTCCCAC
genomic: AGTCTGGGGCGGTATCCAAGGGCTACAACTTTGCATCCACTTGGGAACAGgttggtcgcc ... ccttttacagAGCGCGCCGCTCACGGAGCAGCAGAAGGCCGCGATCGCCGCGCTCTCCCAC
EST: gi|211087683|gb|FL052580.1|FL052580
EST:     AGTCTGGGGCGGTATCCAAGGGCTACAACTTTGCATCCACTTGGGAACAG                         AGCGCGCCGCTCACGGAGCACCAGAAGGCCGCGATCGCCGCGCTCTCCCAC
genomic: AGTCTGGGGCGGTATCCAAGGGCTACAACTTTGCATCCACTTGGGAACAGgttggtcgcc ... ccttttacagAGCGCGCCGCTCACGGAGCAGCAGAAGGCCGCGATCGCCGCGCTCTCCCAC
EST: gi|211087681|gb|FL052578.1|FL052578
EST:     AGTCTGGGGCGGTATCCAAGGGCTACAACTTTGCATCCACTTGGGAACAG                         AGCGCGCCGCTCACGGAGCAGCAGAAGGCCGCGATCGCCGCGCTCTCCCAC
genomic: AGTCTGGGGCGGTATCCAAGGGCTACAACTTTGCATCCACTTGGGAACAGgttggtcgcc ... ccttttacagAGCGCGCCGCTCACGGAGCAGCAGAAGGCCGCGATCGCCGCGCTCTCCCAC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 211

CGCGCCCATGGCGACGCCGCCGCCGGCGGCGACGGCGTCCGCGCTTCCCAAGTCTGGGGCGGTATCCAAGGGCTACAACTTTGCATCCACTTGGGAACAGgttggtcgcc ... ccttttacagAGCGCGCCGCTCACGGAGCAGCAGAAGGCCGCGATCGCCGCGCTCTCCCACGCCGTGGCGGAGCGGCCATTCCCGCCCAACCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 131

CGCGCCCATGGCGACGCCGCCGCCGGCGGCGACGGCGTCCGCGCTTCCCAAGTCTGGGGCGGTATCCAAGGGCTACAACTTTGCATCCACTTGGGAACAGgttggtcgcc ... ccttttacagAGCGCGCCGCTCACGGAGCAGCAGAAGGCCGCGATCGCCGCGCTCTCCCACGCCGTGGCGGAGCGGCCATTCCCGCCCAACCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 210

CGCGCCCATGGCGACGCCGCCGCCGGCGGCGACGGCGTCCGCGCTTCCCAAGTCTGGGGCGGTATCCAAGGGCTACAACTTTGCATCCACTTGGGAACAGgttggtcgcc ... ccttttacagAGCGCGCCGCTCACGGAGCAGCAGAAGGCCGCGATCGCCGCGCTCTCCCACGCCGTGGCGGAGCGGCCATTCCCGCCCAACCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 154

CGCGCCCATGGCGACGCCGCCGCCGGCGGCGACGGCGTCCGCGCTTCCCAAGTCTGGGGCGGTATCCAAGGGCTACAACTTTGCATCCACTTGGGAACAGgttggtcgcc ... ccttttacagAGCGCGCCGCTCACGGAGCAGCAGAAGGCCGCGATCGCCGCGCTCTCCCACGCCGTGGCGGAGCGGCCATTCCCGCCCAACCTG